- Intro to functional genomics assays to study transcriptional regulation and epigenetics
- ChIP-seq and beyond
- R Bioconductor infrastructure for analysis of genomic data
April 4, 2019
File names for most large files, as placeholders
fastq-dump -I --gzip -A SRR1186971
#!/bin/bash
for fileid in SRR1186971 SRR1186973 SRR1186974 SRR1186976
do
fastq-dump -I --gzip -A $fileid
done
https://github.com/qbio-gsk/qbio-gsk/tree/master/2019/lab8/data/chipseq-fastq
bowtie2 -p 10 -t --no-unal -X 500 -x mm10-bowtie2index/mm10 -U SRR1186971.fastq.gz >SRR1186971.sam 2>.bowtie2.SRR1186971
Time loading reference: 00:00:00
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:00
Multiseed full-index search: 00:04:06
24505004 reads; of these:
24505004 (100.00%) were unpaired; of these:
2832435 (11.56%) aligned 0 times
13902816 (56.73%) aligned exactly 1 time
7769753 (31.71%) aligned >1 times
88.44% overall alignment rate
Time searching: 00:04:08
Overall time: 00:04:08
https://github.com/qbio-gsk/qbio-gsk/blob/master/2019/lab8/align/run-alignment.sh
https://github.com/qbio-gsk/qbio-gsk/blob/master/2019/lab8/align/rename-samples.sh
https://github.com/qbio-gsk/qbio-gsk/tree/master/2019/lab8/data/chipseq-bam
macs2 callpeak -t foxp3_rep1.bam -c foxp3_input.bam -f BAM -n foxp3_rep1 -B --SPMR --outdir peaks-macs2/foxp3_rep1/ -g mm -p 0.1 --keep-dup 'auto' --call-summits 2>.macs
idr --verbose --samples foxp3_rep1_peaks.narrowPeak foxp3_rep1_peaks.narrowPeak -o foxp3_rep1_foxp3_rep2.narrowPeak --log-output-file $idrdir/$prefix.log.txt --plot
https://github.com/qbio-gsk/qbio-gsk/tree/master/2019/lab8/peakcalling
(Some) Proteins bind to DNA in a sequence-specific manner
Integrative Genomics Viewer (IGV)
UCSC Genome Browser